From bafaa481386464b47cced3b6a3545aff6d5b9fb2 Mon Sep 17 00:00:00 2001 From: Jenny Medina Date: Thu, 3 Oct 2024 13:44:27 -0400 Subject: [PATCH] Add note on LD_LIBRARY_PATH to install instructions for Conda --- docs/tutorials/installation.md | 23 +++++++++++++++++++++-- 1 file changed, 21 insertions(+), 2 deletions(-) diff --git a/docs/tutorials/installation.md b/docs/tutorials/installation.md index 66b090708..f80fba103 100644 --- a/docs/tutorials/installation.md +++ b/docs/tutorials/installation.md @@ -2,7 +2,18 @@ By following the instructions below, you are installing the `synapseclient`, `synapseutils` and the command line client. -## PyPI +## TL;DR For Experts +1. Set up your Python development environment in your preferred manner (e.g. with `conda`, `pyenv`, etc). +2. Run +``` +pip install --upgrade synapseclient +``` +3. Verify your installation +``` +pip show synapseclient +``` + +## Installation Guide For: PyPI Users The [synapseclient](https://pypi.python.org/pypi/synapseclient/) package is available from PyPI. It can be installed or upgraded with pip. Due to the nature of Python, we highly recommend you set up your python environment with [conda](https://www.anaconda.com/products/distribution) or [pyenv](https://github.com/pyenv/pyenv) and create virtual environments to control your Python dependencies for your work. @@ -20,6 +31,14 @@ pip install --upgrade "synapseclient[pandas]" pip install --upgrade "synapseclient[pandas, pysftp, boto3]" ``` +> **NOTE**
+> The `synapseclient` package may require loading shared libraries located in your system's `/usr/local/lib` directory. Some users working +with `conda` have experienced issues with shared libraries not being found due to the system searching in the wrong locations. Although +not recommended, one solution for this is manually configuring the `LD_LIBRARY_PATH` environment variable to point +to the `/usr/local/lib` directory. [See here](https://github.com/conda/conda/issues/12800) for more context on this solution, and for alternatives. + +---- + - pyenv: Use [virtualenv](https://virtualenv.pypa.io/en/latest/) to manage your python environment: ```bash @@ -42,7 +61,7 @@ python3 -m pip3 install --upgrade "synapseclient[pandas, pysftp, boto3]" The dependencies on pandas, pysftp, and boto3 are optional. The Synapse `synapseclient.table` feature integrates with Pandas. Support for sftp is required for users of SFTP file storage. Both require native libraries to be compiled or installed separately from prebuilt binaries. -## Local +## Installation Guide For: Git Users Source code and development versions are [available on Github](https://github.com/Sage-Bionetworks/synapsePythonClient). Installing from source: